Module 4: Ecology Description: Studying the population dynamics of groups of organisms provides an example of how physics (nonlinear dynamics, ODEs, limit cycles, chaos, etc.) can be used to gain further insight into fundamental biological processes. Rotifer-algae culture imaged with 10X microscope objective lens. Predator-prey population dynamics of rotifer-algae cultures Goal: Maintain rotifer population in an algae culture in order to observe predator-prey dynamics between the two species. Materials Resting eggs (Brachionus manjavacas) 2L algae (Tetraselmis suecica) 2L 15ppt ASW (artificial salt water) 2L 15ppt F media Nephelo flask (2) Test tubes Double air pump Glass rod (hollow) (2) Plastic tubing Gang valve (2) Small petri dish Parafilm 1.7mL pipettes DIY incubator Fluorescent lightbulb MicroSD card MicroSD card adapter MicroSD transflash breakout board
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Predator-prey population dynamics of rotifer-algae cultures 4/Module4...Rotifer-algae culture imaged with 10X microscope objective lens. Predator-prey population dynamics of rotifer-algae
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Module 4: Ecology
Description: Studying the population dynamics of groups of organisms provides an example of how physics (nonlinear dynamics, ODEs, limit cycles, chaos, etc.) can be used to gain further insight into fundamental biological processes.
Rotifer-algae culture imaged with 10X microscope objective lens.
Predator-prey population dynamics of
rotifer-algae cultures Goal: Maintain rotifer population in an algae culture in order to observe predator-prey dynamics between the two species.
1. Measure out 15g/L of salt (adjust according to desired volume). 2. Add salt to required volume of DI water and stir until dissolved. 3. Check the salinity using the refractometer with 20uL of ASW. 4. Adjust salt concentration/water volume as needed.
15ppt F Media preparation
1. Measure out and add chemicals according to the chart below (metal and vitamin solutions are stored at 4 deg C).
2. Mix media until all ingredients are dissolved.
3. 1L 2L 5L
Sea salts 15g 30g 75g
KNO3 150mg 300mg 750mg
NaH2PO4 5mg 10mg 25mg
Metals 2mL 4mL 10mL
Vitamins 2mL 4mL 10mL
Hatching protocol
1. Put 15ppt ASW into a small petri dish (enough to cover the bottom). 2. Put resting eggs into the petri dish and label with name, date, and time. 3. Place the petri dish under fluorescent light and leave eggs to hatch overnight (~16hrs). 4. Adjust shaking incubator settings to maintain room temperature (25-28 deg C), provide
constant light, and write the light sensor data to an SD card (details below).
Culturing protocols
Our algae was cultured in F media, so all cultures are essentially 100% F media, but the given percentage of algae represents the initial prey population.
Experiment 1: Predator-prey observation
Objective:
1. Prepare a 150mL culture of 75% F media and 25% algae. 2. Aliquot 125mL into a Nephelo flasks and 25mL into a test tube and cover the tops of both
containers with parafilm. 3. Attach one end of the plastic tubing to the air pump using a gang valve and the other end to
a glass rod. 4. Poke a hole in the parafilm and aerate both cultures with an air pump (flask and test tube).
a. For algae only: set the gang valve so that the airflow is medium-high (culture should be bubbling).
b. For rotifers in algae culture: set the gang valve so that airflow is low (only one or two visible bubbles).
5. Once rotifers have hatched, use a pipette and an empty petri dish to count and place ~50 rotifers in the Nephelo flask.
a. At this point, all rotifers are female; after four days, new resting eggs will be produced.
Experiment 2: Light Variation
Objective:
1. Prepare a 250mL culture of 75% F media and 25% algae. 2. Aliquot 125mL into two Nephelo flasks and cover the tops of both containers with parafilm. 3. Attach one end of the plastic tubing to the air pump using a gang valve and the other end to
a glass rod. 4. Poke a hole in the parafilm and aerate both cultures with an air pump (flask and test tube).
a. For algae only: set the gang valve so that the airflow is medium-high (culture should be bubbling).
b. For rotifers in algae culture: set the gang valve so that airflow is low (only one or two visible bubbles).
5. Once rotifers have hatched, use a pipette and an empty petri dish to count and place ~50 rotifers in each Nephelo flask.
a. At this point, all rotifers are female; after four days, new resting eggs will be produced.
6. Place one culture under fluorescent light bulb and cover the other to hide it from the light (both inside incubator).
Experiment 3: Population variation
Objective:
Prepare a 250mL culture of 75% F media and 25% algae.
Aliquot 125mL into two Nephelo flasks and cover the tops of both containers with parafilm.
Attach one end of the plastic tubing to the air pump using a gang valve and the other end to a glass rod.
Poke a hole in the parafilm and aerate both cultures with an air pump (flask and test tube). o For algae only: set the gang valve so that the airflow is medium-high (culture should
be bubbling).
o For rotifers in algae culture: set the gang valve so that airflow is low (only one or two visible bubbles).
Once rotifers have hatched, use a pipette and an empty petri dish to count and place ~50 rotifers in one Nephelo flask.
o At this point, all rotifers are female; after four days, new resting eggs will be produced.
Place both cultures under fluorescent light bulb inside the incubator.
Experiment 4: Predator population variation
Objective:
1. Prepare a 250mL culture of 75% F media and 25% algae. 2. Aliquot 125mL into two Nephelo flasks and cover the tops of both containers with parafilm. 3. Attach one end of the plastic tubing to the air pump using a gang valve and the other end to
a glass rod. 4. Poke a hole in the parafilm and aerate both cultures with an air pump (flask and test tube).
a. For algae only: set the gang valve so that the airflow is medium-high (culture should be bubbling).
b. For rotifers in algae culture: set the gang valve so that airflow is low (only one or two visible bubbles).
5. Once rotifers have hatched, use a pipette and an empty petri dish to count and place ~10 rotifers in one Nephelo flask and ~50 in the other.
a. At this point, all rotifers are female; after four days, new resting eggs will be produced.
6. Place both cultures under fluorescent light bulb inside the incubator.
Experiment 5: Prey population variation
Objective:
1. Prepare two 125mL cultures one of 75% F media and 25% algae and one of 50% F media and 50% algae.
2. Aliquot each culture into a Nephelo flask and cover the tops of both containers with parafilm. 3. Attach one end of the plastic tubing to the air pump using a gang valve and the other end to
a glass rod. 4. Poke a hole in the parafilm and aerate both cultures with an air pump (flask and test tube).
a. For algae only: set the gang valve so that the airflow is medium-high (culture should be bubbling).
b. For rotifers in algae culture: set the gang valve so that airflow is low (only one or two visible bubbles).
5. Once rotifers have hatched, use a pipette and an empty petri dish to count and place ~10 rotifers in each Nephelo flask.
a. At this point, all rotifers are female; after four days, new resting eggs will be produced.
6. Place both cultures under fluorescent light bulb inside the incubator.
Experimental set-up
Additions to shaking incubator
(optional) Ambient light sensor (TEMT6000) to track the relative algae concentration, measured by the "greenness" of the flask.
Temperature sensor (TMP36) used to maintain ambient temperature (25-28 deg C).
Light and temperature sensor data is written to a text file on a microSD card.
Replace incandescent lightbulb with a fluorescent lightbulb and change the relay settings so that the culture receives constant light.
Arduino code
with TEMT6000:
#include <SPI.h>
#include <SD.h>
#include <Servo.h>
//TMP36 Pin Variables
int sensorPin = 0; //the analog pin the TMP36's Vout (sense) pin is connected
to
//the resolution is 10 mV / degree centigrade with a
//500 mV offset to allow for negative temperatures